protocols::rna::denovo::movers::RNA_DeNovoProtocolMover Class Reference

#include <RNA_DeNovoProtocolMover.hh>

Inheritance diagram for protocols::rna::denovo::movers::RNA_DeNovoProtocolMover:

Public Member Functions
	RNA_DeNovoProtocolMover ()
	~RNA_DeNovoProtocolMover () override
void	apply (core::pose::Pose &pose) override
	Main Method. More...
moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...
moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...
void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
std::string	get_name () const override
	Each derived class must specify its name. The class name. More...
core::import_pose::options::RNA_DeNovoProtocolOptionsCOP	options () const
core::import_pose::RNA_DeNovoParametersCOP	rna_params () const
void	set_fasta_files (utility::vector1< std::string > const &fasta_files)
void	set_input_pdbs (utility::vector1< std::string > const &input_pdbs)
void	set_input_silent_files (utility::vector1< std::string > const &input_silent_files)
void	set_sequence_strings (utility::vector1< std::string > const &sequence_strings)
void	set_minimize_rna (bool const minimize_rna)
void	set_helical_substructs (utility::vector1< std::string > const &helical_substructs)
void	set_dock_chunks (utility::vector1< std::string > const &dock_chunks)
void	set_input_initialization_pdbs (utility::vector1< std::string > const &input_initialization_pdbs)
void	set_align_pdb (std::string const &align_pdb)
void	set_nstruct (Size const nstruct)
void	set_silent_file (std::string const &silent_file)
void	de_novo_setup_from_command_line ()
void	de_novo_setup_from_options (utility::options::OptionCollection const &opts)
void	de_novo_setup_from_tag (utility::tag::TagCOP const &tag)
void	set_protocol_options (core::import_pose::options::RNA_DeNovoProtocolOptionsOP const &protocol_options)
void	set_residue_type_set (core::chemical::ResidueTypeSetCOP const &rts)
Public Member Functions inherited from protocols::moves::Mover
	Mover ()
virtual MoverOP	create ()
MoverCOP	get_self_ptr () const
MoverOP	get_self_ptr ()
MoverCAP	get_self_weak_ptr () const
MoverAP	get_self_weak_ptr ()
	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...
virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...
virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...
MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...
void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...
virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...
void	set_type (std::string const &setting)
	Set the 'type' string. More...
std::string	get_type () const
void	type (const std::string &type_in)
	Set the 'type' string. More...
std::string const &	type () const
	Get the set 'type' string. More...
virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...
virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
PoseCOP	get_input_pose () const
PoseCOP	get_native_pose () const
void	set_current_job (protocols::jobdist::BasicJobCOP job)
jobdist::BasicJobCOP	get_current_job () const
virtual void	set_current_tag (std::string const &new_tag)
std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...
virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...
virtual core::Real	last_proposal_density_ratio ()
virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...
virtual Strings &	info ()
	non-const accessor More...
virtual Strings const &	info () const
	const accessor More...
virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions
static std::string	mover_name ()
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
static void	list_options_read (utility::options::OptionKeyList &opts)
Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()
static void	register_options ()
	Overload this static method if you access options within the mover. More...

Private Types
using	Size = core::Size

Private Member Functions
void	initialize_scorefxn (core::pose::Pose &pose)
void	initialize_sequence_information (int const offset, bool const edensity_mapfile_provided, bool const rna_protein_docking, bool const virtual_anchor_provided, bool const cutpoint_open_provided, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &possible_cutpoint_open_numbering, core::pose::full_model_info::FullModelParametersOP &full_model_parameters, utility::vector1< core::Size > &cutpoint_open_in_full_model)
void	check_secstructs (bool const modeling_with_density, bool const rna_protein_docking, std::string const &sequence, core::pose::rna::RNA_SecStruct const &secstruct, core::pose::rna::RNA_SecStruct const &secstruct_general)
void	input_numbering_setup (std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &input_res_resnum_and_chain, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &input_silent_res_resnum_and_chain, std::string const &sequence, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > &input_res, utility::vector1< utility::vector1< int > > &resnum_list, utility::vector1< core::Size > &input_res_initialize, utility::vector1< utility::vector1< core::Size > > &helical_substruct_res, utility::vector1< core::Size > &dock_chunks_res)
void	input_pdb_numbering_setup (std::string const &sequence, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > &input_res, utility::vector1< utility::vector1< core::Size > > &helical_substruct_res, utility::vector1< core::Size > &dock_chunks_res, utility::vector1< utility::vector1< int > > &resnum_list, utility::vector1< core::Size > &input_res_user_defined, Size &input_res_user_defined_count)
void	input_initialization_pdb_numbering_setup (std::string const &sequence, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > &input_initialization_res)
void	input_silent_numbering_setup (std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &input_silent_res_resnum_and_chain, std::string const &sequence, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > const &input_res_user_defined, core::Size const &input_res_user_defined_count, utility::vector1< core::Size > &input_res, utility::vector1< utility::vector1< core::Size > > &helical_substruct_res, utility::vector1< core::Size > &dock_chunks_res, utility::vector1< utility::vector1< int > > &resnum_list)
void	setup_obligate_pair (std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &extra_minimize_res, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< utility::vector1< int > > const &resnum_list, core::pose::rna::RNA_SecStruct const &secstruct, core::pose::rna::RNA_SecStruct const &secstruct_general, utility::vector1< core::Size > const &cutpoint_open_in_full_model, utility::vector1< core::Size > &obligate_pair, utility::vector1< std::string > &obligate_pair_explicit, utility::vector1< core::Size > &domain_map)
void	initial_pose_setup (std::string const &in_path, bool const lores_sfxn_provided, bool const native_provided, bool const edensity_mapfile_provided, bool const working_native_provided, std::string const &working_native, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > const &working_res, core::pose::Pose &full_pose, bool &is_rna_and_protein)
void	constraint_setup (bool const constraint_file_provided, std::string const &constraint_file, utility::vector1< core::Size > const &working_res, core::pose::Pose &full_pose)
void	refine_working_obligate_pairs (std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &remove_obligate_pair_rc, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > const &obligate_pair, utility::vector1< std::string > &obligate_pair_explicit, utility::vector1< core::Size > const &working_res, utility::vector1< core::pose::rna::BasePair > &working_obligate_pairs)
void	setup_working_chain_connections (utility::vector1< std::string > const &chain_connections, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters, utility::vector1< core::Size > const &working_res, utility::vector1< std::pair< utility::vector1< core::Size >, utility::vector1< core::Size > > > &working_chain_connections)
void	setup_pairing_sets (utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &working_stems, utility::vector1< core::pose::rna::BasePair > &working_obligate_pairs, core::pose::rna::RNA_BasePairList &rna_pairing_list, utility::vector1< utility::vector1< core::Size > > &working_obligate_pair_sets, utility::vector1< utility::vector1< core::Size > > &working_stem_pairing_sets)
void	setup_ft_from_silent (bool const ft_from_silent_provided, std::string const &ft_silent_file, bool const tag_provided, utility::vector1< std::string > const &tag, bool &use_fold_tree_from_silent_file, core::kinematics::FoldTree &fold_tree_from_silent_file)
void	setup_final_res_lists (utility::vector1< core::Size > const &working_res, utility::vector1< core::Size > const &cutpoint_open_in_full_model, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &extra_minimize_res_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &extra_minimize_chi_res_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &output_jump_res_rc, bool const minimize_rna_specified, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &syn_chi_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &anti_chi_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &block_stack_above_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &block_stack_below_rc, core::pose::full_model_info::FullModelParametersOP const &full_model_parameters)
utility::vector1< core::Size >	working_res_map (utility::vector1< core::Size > const &vec, utility::vector1< core::Size > const &working_res, bool const leave_out_last_working_residue=false) const
std::string	working_res_map (std::string const &seq, utility::vector1< core::Size > const &working_res, bool const annotations_in_brackets=true) const
core::pose::rna::RNA_SecStruct	working_res_map (core::pose::rna::RNA_SecStruct const &seq, utility::vector1< core::Size > const &working_res) const
void	get_seq_and_resnum (std::string const &pdb, std::string &seq, utility::vector1< int > &resnum, utility::vector1< char > &chain, utility::vector1< std::string > &segid) const
std::string	get_silent_seq (std::string const &silent_file) const
std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > >	get_silent_resnum (std::string const &silent_file) const
bool	already_listed_in_obligate_pair (utility::vector1< core::Size > const &new_pair, utility::vector1< core::Size > const &obligate_pair) const
bool	already_listed_in_obligate_pair (utility::vector1< Size > const &new_pair, utility::vector1< Size > const &obligate_pair, utility::vector1< Size > const &obligate_pair_explicit) const
void	update_working_obligate_pairs_with_stems (utility::vector1< core::pose::rna::BasePair > &working_obligate_pairs, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &working_stems, utility::vector1< core::Size > const &working_input_res) const
core::pose::PoseOP	get_native_pose ()
void	add_chem_shift_info (core::pose::Pose &not_very_const_pose) const

Private Attributes
core::import_pose::options::RNA_DeNovoProtocolOptionsOP	options_
core::import_pose::RNA_DeNovoParametersOP	rna_params_
core::chemical::ResidueTypeSetCOP	rsd_set_
core::pose::PoseOP	pose_
core::pose::PoseOP	native_pose_
utility::vector1< std::string >	fasta_files_
utility::vector1< std::string >	input_pdbs_
utility::vector1< std::string >	input_silent_files_
utility::vector1< std::string >	sequence_strings_
bool	minimize_rna_
bool	minimize_rna_has_been_specified_ = false
utility::vector1< std::string >	helical_substructs_
utility::vector1< std::string >	dock_chunks_
utility::vector1< std::string >	input_initialization_pdbs_
protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP	vdw_grid_
RNA_FragmentMonteCarloOP	rna_fragment_monte_carlo_
core::scoring::ScoreFunctionOP	denovo_scorefxn_
core::scoring::ScoreFunctionOP	hires_scorefxn_
std::list< core::Real >	all_lores_score_final_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP
typedef core::pose::Pose	Pose
typedef core::pose::PoseCOP	PoseCOP
typedef std::list< std::string >	Strings
Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Member Typedef Documentation

Size

using protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::Size = core::Size

private

Constructor & Destructor Documentation

RNA_DeNovoProtocolMover()

protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::RNA_DeNovoProtocolMover

(

)

~RNA_DeNovoProtocolMover()

protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::~RNA_DeNovoProtocolMover ( )

overridedefault

Member Function Documentation

add_chem_shift_info()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::add_chem_shift_info ( core::pose::Pose &  not_very_const_pose ) const

private

References core::pose::Pose::energies(), core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential::get_total_exp_chemical_shift_data_points(), core::scoring::rna_chem_shift, core::pose::setPoseExtraScore(), and core::scoring::Energies::total_energies().

already_listed_in_obligate_pair() [1/2]

bool protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::already_listed_in_obligate_pair ( utility::vector1< core::Size > const &  new_pair, utility::vector1< core::Size > const &  obligate_pair  ) const

private

already_listed_in_obligate_pair() [2/2]

bool protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::already_listed_in_obligate_pair ( utility::vector1< Size > const &  new_pair, utility::vector1< Size > const &  obligate_pair, utility::vector1< Size > const &  obligate_pair_explicit  ) const

private

apply()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::apply ( core::pose::Pose &  )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::viewer::add_conformation_viewer(), core::pose::rna::add_number_base_pairs(), core::pose::rna::add_number_native_base_pairs(), protocols::viewer::clear_conformation_viewers(), core::pose::Pose::conformation(), core::pose::Pose::dump_pdb(), protocols::scoring::fill_vdw_cached_rep_screen_info_from_command_line(), protocols::constraint_generator::get_native_pose(), protocols::jd2::output_intermediate_pose(), core::pose::setPoseExtraScore(), and core::chemical::rna::TR().

check_secstructs()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::check_secstructs ( bool const  modeling_with_density, bool const  rna_protein_docking, std::string const &  sequence, core::pose::rna::RNA_SecStruct const &  secstruct, core::pose::rna::RNA_SecStruct const &  secstruct_general  )

private

References core::pose::rna::RNA_SecStruct::blank(), and core::pose::rna::RNA_SecStruct::check_compatible_with_sequence().

clone()

moves::MoverOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::clone ( ) const

overridevirtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

constraint_setup()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::constraint_setup ( bool const  constraint_file_provided, std::string const &  constraint_file, utility::vector1< core::Size > const &  working_res, core::pose::Pose &  full_pose  )

private

References core::pose::Pose::constraint_set(), and core::conformation::named_atom_id_to_atom_id().

de_novo_setup_from_command_line()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_command_line

(

)

de_novo_setup_from_options()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_options

(

utility::options::OptionCollection const &

opts

)

References core::pose::rna::RNA_SecStruct::blank(), core::io::rna::RNA_DataReader::fill_rna_data_info(), core::pose::copydofs::FIXED_DOMAIN, core::pose::full_model_info::INPUT_DOMAIN, protocols::hybridization::path, core::pose::rna::RNA_SecStruct::remove_pair(), core::pose::rna::RNA_SecStruct::secstruct(), core::pose::full_model_info::set_full_model_info(), core::pose::rna::RNA_SecStruct::stems(), and core::chemical::rna::TR().

de_novo_setup_from_tag()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::de_novo_setup_from_tag

(

utility::tag::TagCOP const &

tag

)

References core::pose::rna::RNA_SecStruct::blank(), core::io::rna::RNA_DataReader::fill_rna_data_info(), core::pose::copydofs::FIXED_DOMAIN, core::pose::full_model_info::INPUT_DOMAIN, core::pose::rna::RNA_SecStruct::remove_pair(), core::pose::rna::RNA_SecStruct::secstruct(), core::pose::full_model_info::set_full_model_info(), core::pose::rna::RNA_SecStruct::stems(), and core::chemical::rna::TR().

fresh_instance()

moves::MoverOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::fresh_instance ( ) const

overridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

get_name()

std::string protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

get_native_pose()

core::pose::PoseOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::get_native_pose ( )

inlineprivate

References native_pose_.

get_seq_and_resnum()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::get_seq_and_resnum ( std::string const &  pdb, std::string &  seq, utility::vector1< int > &  resnum, utility::vector1< char > &  chain, utility::vector1< std::string > &  segid  ) const

private

References core::pose::Pose::pdb_info(), core::import_pose::pose_from_file(), core::pose::Pose::sequence(), and core::pose::Pose::size().

get_silent_resnum()

std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::get_silent_resnum ( std::string const &  silent_file ) const

private

References core::io::silent::SilentFileData::get_resnum().

get_silent_seq()

std::string protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::get_silent_seq ( std::string const &  silent_file ) const

private

References core::io::silent::SilentFileData::get_sequence().

initial_pose_setup()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initial_pose_setup ( std::string const &  in_path, bool const  lores_sfxn_provided, bool const  native_provided, bool const  edensity_mapfile_provided, bool const  working_native_provided, std::string const &  working_native, core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters, utility::vector1< core::Size > const &  working_res, core::pose::Pose &  full_pose, bool &  is_rna_and_protein  )

private

References core::pose::addVirtualResAsRoot(), core::import_pose::initialize_native_and_align_pose(), core::conformation::Residue::is_protein(), core::pose::make_pose_from_sequence(), core::import_pose::PDB_file, core::pose::pdbslice(), core::import_pose::pose_from_file(), core::pose::Pose::residue(), core::pose::Pose::sequence(), core::pose::set_output_res_and_chain(), core::pose::Pose::total_residue(), and core::chemical::rna::TR().

initialize_scorefxn()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initialize_scorefxn ( core::pose::Pose &  pose )

private

References core::scoring::apply_set_weights(), core::scoring::atom_pair_constraint, core::scoring::base_pair_constraint, core::scoring::chainbreak, core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, core::scoring::elec_dens_fast, protocols::rna::denovo::get_rna_hires_scorefxn(), core::scoring::grid_vdw, core::scoring::linear_chainbreak, core::scoring::rna::nonconst_rna_scoring_info_from_pose(), and core::scoring::rna_chem_map_lores.

initialize_sequence_information()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::initialize_sequence_information ( int const  offset, bool const  edensity_mapfile_provided, bool const  rna_protein_docking, bool const  virtual_anchor_provided, bool const  cutpoint_open_provided, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  possible_cutpoint_open_numbering, core::pose::full_model_info::FullModelParametersOP &  full_model_parameters, utility::vector1< core::Size > &  cutpoint_open_in_full_model  )

private

References core::chemical::chr_chains(), core::import_pose::get_extra_cutpoints_from_names(), core::import_pose::get_sequence_information(), core::sequence::parse_out_non_standard_residues(), core::sequence::strip_spacers(), and core::chemical::rna::TR().

input_initialization_pdb_numbering_setup()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_initialization_pdb_numbering_setup ( std::string const &  sequence, core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters, utility::vector1< core::Size > &  input_initialization_res  )

private

References core::chemical::rings::q, and core::chemical::rna::TR().

input_numbering_setup()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_numbering_setup ( std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  input_res_resnum_and_chain, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  input_silent_res_resnum_and_chain, std::string const &  sequence, core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters, utility::vector1< core::Size > &  input_res, utility::vector1< utility::vector1< int > > &  resnum_list, utility::vector1< core::Size > &  input_res_initialize, utility::vector1< utility::vector1< core::Size > > &  helical_substruct_res, utility::vector1< core::Size > &  dock_chunks_res  )

private

input_pdb_numbering_setup()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_pdb_numbering_setup ( std::string const &  sequence, core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters, utility::vector1< core::Size > &  input_res, utility::vector1< utility::vector1< core::Size > > &  helical_substruct_res, utility::vector1< core::Size > &  dock_chunks_res, utility::vector1< utility::vector1< int > > &  resnum_list, utility::vector1< core::Size > &  input_res_user_defined, Size &  input_res_user_defined_count  )

private

References core::chemical::rings::q, and core::chemical::rna::TR().

input_silent_numbering_setup()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_silent_numbering_setup ( std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  input_silent_res_resnum_and_chain, std::string const &  sequence, core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters, utility::vector1< core::Size > const &  input_res_user_defined, core::Size const &  input_res_user_defined_count, utility::vector1< core::Size > &  input_res, utility::vector1< utility::vector1< core::Size > > &  helical_substruct_res, utility::vector1< core::Size > &  dock_chunks_res, utility::vector1< utility::vector1< int > > &  resnum_list  )

private

References core::chemical::rings::q, and core::chemical::rna::TR().

list_options_read()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::list_options_read ( utility::options::OptionKeyList &  opts )

static

References core::import_pose::dump_stems(), and protocols::hybridization::path.

mover_name()

std::string protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::mover_name ( )

static

options()

core::import_pose::options::RNA_DeNovoProtocolOptionsCOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::options ( ) const

inline

References options_.

parse_my_tag()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::parse_my_tag ( utility::tag::TagCOP  tag, basic::datacache::DataMap &  data  )

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References core::chemical::FA_STANDARD.

provide_xml_schema()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References core::import_pose::options::RNA_DeNovoProtocolOptions::list_attributes(), and protocols::moves::xsd_type_definition_w_attributes().

refine_working_obligate_pairs()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::refine_working_obligate_pairs ( std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  remove_obligate_pair_rc, core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters, utility::vector1< core::Size > const &  obligate_pair, utility::vector1< std::string > &  obligate_pair_explicit, utility::vector1< core::Size > const &  working_res, utility::vector1< core::pose::rna::BasePair > &  working_obligate_pairs  )

private

References core::chemical::rna::ANY_BASE_DOUBLET_ORIENTATION, core::chemical::rna::ANY_BASE_EDGE, core::pose::rna::get_base_doublet_orientation_from_LW(), core::chemical::rna::get_edge_from_char(), core::chemical::rna::get_LW_orientation_from_char(), core::chemical::rna::get_orientation_from_char(), and core::chemical::rings::q.

rna_params()

core::import_pose::RNA_DeNovoParametersCOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::rna_params ( ) const

inline

References rna_params_.

set_align_pdb()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_align_pdb

(

std::string const &

align_pdb

)

set_dock_chunks()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_dock_chunks ( utility::vector1< std::string > const &  dock_chunks )

inline

References dock_chunks_.

set_fasta_files()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_fasta_files ( utility::vector1< std::string > const &  fasta_files )

inline

References fasta_files_.

set_helical_substructs()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_helical_substructs ( utility::vector1< std::string > const &  helical_substructs )

inline

References helical_substructs_.

set_input_initialization_pdbs()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_input_initialization_pdbs

(

utility::vector1< std::string > const &

input_initialization_pdbs

)

set_input_pdbs()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_input_pdbs

(

utility::vector1< std::string > const &

input_pdbs

)

set_input_silent_files()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_input_silent_files

(

utility::vector1< std::string > const &

input_silent_files

)

set_minimize_rna()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_minimize_rna ( bool const  minimize_rna )

inline

References minimize_rna_, and minimize_rna_has_been_specified_.

set_nstruct()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_nstruct

(

Size const

nstruct

)

set_protocol_options()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_protocol_options ( core::import_pose::options::RNA_DeNovoProtocolOptionsOP const &  protocol_options )

inline

References options_.

set_residue_type_set()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_residue_type_set ( core::chemical::ResidueTypeSetCOP const &  rts )

inline

References rsd_set_.

set_sequence_strings()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_sequence_strings ( utility::vector1< std::string > const &  sequence_strings )

inline

References sequence_strings_.

set_silent_file()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::set_silent_file

(

std::string const &

silent_file

)

setup_final_res_lists()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::setup_final_res_lists ( utility::vector1< core::Size > const &  working_res, utility::vector1< core::Size > const &  cutpoint_open_in_full_model, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  extra_minimize_res_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  extra_minimize_chi_res_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  output_jump_res_rc, bool const  minimize_rna_specified, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  syn_chi_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  anti_chi_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  block_stack_above_rc, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  block_stack_below_rc, core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters  )

private

References core::pose::full_model_info::CUTPOINT_OPEN, core::pose::full_model_info::EXTRA_MINIMIZE, core::pose::full_model_info::RNA_ANTI_CHI, core::pose::full_model_info::RNA_BLOCK_STACK_ABOVE, core::pose::full_model_info::RNA_BLOCK_STACK_BELOW, core::pose::full_model_info::RNA_SYN_CHI, and core::chemical::rna::TR().

setup_ft_from_silent()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::setup_ft_from_silent ( bool const  ft_from_silent_provided, std::string const &  ft_silent_file, bool const  tag_provided, utility::vector1< std::string > const &  tag, bool &  use_fold_tree_from_silent_file, core::kinematics::FoldTree &  fold_tree_from_silent_file  )

private

setup_obligate_pair()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::setup_obligate_pair ( std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  extra_minimize_res, core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters, utility::vector1< utility::vector1< int > > const &  resnum_list, core::pose::rna::RNA_SecStruct const &  secstruct, core::pose::rna::RNA_SecStruct const &  secstruct_general, utility::vector1< core::Size > const &  cutpoint_open_in_full_model, utility::vector1< core::Size > &  obligate_pair, utility::vector1< std::string > &  obligate_pair_explicit, utility::vector1< core::Size > &  domain_map  )

private

References core::pose::rna::RNA_SecStruct::base_pairs(), protocols::mean_field::max(), protocols::mean_field::min(), and core::chemical::rings::q.

setup_pairing_sets()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::setup_pairing_sets ( utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &  working_stems, utility::vector1< core::pose::rna::BasePair > &  working_obligate_pairs, core::pose::rna::RNA_BasePairList &  rna_pairing_list, utility::vector1< utility::vector1< core::Size > > &  working_obligate_pair_sets, utility::vector1< utility::vector1< core::Size > > &  working_stem_pairing_sets  )

private

References core::chemical::rna::ANTIPARALLEL, and core::chemical::rna::WATSON_CRICK.

setup_working_chain_connections()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::setup_working_chain_connections ( utility::vector1< std::string > const &  chain_connections, core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters, utility::vector1< core::Size > const &  working_res, utility::vector1< std::pair< utility::vector1< core::Size >, utility::vector1< core::Size > > > &  working_chain_connections  )

private

update_working_obligate_pairs_with_stems()

void protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::update_working_obligate_pairs_with_stems ( utility::vector1< core::pose::rna::BasePair > &  working_obligate_pairs, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &  working_stems, utility::vector1< core::Size > const &  working_input_res  ) const

private

References core::chemical::rna::ANTIPARALLEL, core::scoring::pair, and core::chemical::rna::WATSON_CRICK.

working_res_map() [1/3]

core::pose::rna::RNA_SecStruct protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::working_res_map ( core::pose::rna::RNA_SecStruct const &  seq, utility::vector1< core::Size > const &  working_res  ) const

private

References core::pose::rna::RNA_SecStruct::secstruct().

working_res_map() [2/3]

std::string protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::working_res_map ( std::string const &  seq, utility::vector1< core::Size > const &  working_res, bool const  annotations_in_brackets = true  ) const

private

References core::sequence::strip_spacers().

working_res_map() [3/3]

vector1< Size > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::working_res_map ( utility::vector1< core::Size > const &  vec, utility::vector1< core::Size > const &  working_res, bool const  leave_out_last_working_residue = false  ) const

private

Member Data Documentation

all_lores_score_final_

std::list< core::Real > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::all_lores_score_final_

private

denovo_scorefxn_

core::scoring::ScoreFunctionOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::denovo_scorefxn_

private

dock_chunks_

utility::vector1< std::string > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::dock_chunks_

private

Referenced by set_dock_chunks().

fasta_files_

utility::vector1< std::string > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::fasta_files_

private

Referenced by set_fasta_files().

helical_substructs_

utility::vector1< std::string > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::helical_substructs_

private

Referenced by set_helical_substructs().

hires_scorefxn_

core::scoring::ScoreFunctionOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::hires_scorefxn_

private

input_initialization_pdbs_

utility::vector1< std::string > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_initialization_pdbs_

private

input_pdbs_

utility::vector1< std::string > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_pdbs_

private

input_silent_files_

utility::vector1< std::string > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::input_silent_files_

private

minimize_rna_

bool protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::minimize_rna_

private

Referenced by set_minimize_rna().

minimize_rna_has_been_specified_

bool protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::minimize_rna_has_been_specified_ = false

private

Referenced by set_minimize_rna().

native_pose_

core::pose::PoseOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::native_pose_

private

Referenced by get_native_pose().

options_

core::import_pose::options::RNA_DeNovoProtocolOptionsOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::options_

private

Referenced by options(), and set_protocol_options().

pose_

core::pose::PoseOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::pose_

private

rna_fragment_monte_carlo_

RNA_FragmentMonteCarloOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::rna_fragment_monte_carlo_

private

rna_params_

core::import_pose::RNA_DeNovoParametersOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::rna_params_

private

Referenced by rna_params().

rsd_set_

core::chemical::ResidueTypeSetCOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::rsd_set_

private

Referenced by set_residue_type_set().

sequence_strings_

utility::vector1< std::string > protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::sequence_strings_

private

Referenced by set_sequence_strings().

vdw_grid_

protocols::stepwise::modeler::rna::checker::RNA_VDW_BinCheckerOP protocols::rna::denovo::movers::RNA_DeNovoProtocolMover::vdw_grid_

private

---

The documentation for this class was generated from the following files:

• src/protocols/rna/denovo/movers/RNA_DeNovoProtocolMover.hh
• src/protocols/rna/denovo/movers/RNA_DeNovoProtocolMover.cc